PlotPies: Plot comparison with other clustering

In FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data

Description

Plot FlowSOM grid or tree, with pies indicating another clustering or manual gating result

Usage

PlotPies(
  fsom,
  cellTypes,
  view = "MST",
  colorPalette = grDevices::colorRampPalette(c("white", "#00007F", "blue", "#007FFF",
    "cyan", "#7FFF7F", "yellow", "#FF7F00", "red")),
  backgroundValues = NULL,
  backgroundColor = function(n) {     grDevices::rainbow(n, alpha = 0.3) },
  backgroundLim = NULL,
  backgroundBreaks = NULL,
  legend = TRUE,
  main = ""
)

Arguments

fsom	FlowSOM object, as generated by BuildMST
cellTypes	Array of factors indicating the celltypes
view	Preferred view, options: "MST", "grid" or "tSNE" (if this option was selected while building the MST)
colorPalette	Colorpalette to be used for the markers
backgroundValues	Values to be used for background coloring, either numerical values or something that can be made into a factor (e.g. a clustering)
backgroundColor	Colorpalette to be used for the background coloring . Can be either a function or an array specifying colors
backgroundLim	Only used when backgroundValues are numerical. Defaults to min and max of the backgroundValues.
backgroundBreaks	Breaks to pass on to cut, to split numerical background values. If NULL, the length of backgroundColor will be used (default 100).
legend	Logicle, if T add a legend
main	Title of the plot

Value

Nothing is returned. A plot is drawn in which each node is represented by a pie chart indicating the percentage of cells present of each cell type. At the end, the layout is set to 1 figure again.

See Also

PlotStars,PlotMarker, PlotCenters,BuildMST

Examples

#' # Identify the files
fcs_file <- system.file("extdata", "68983.fcs", package = "FlowSOM")
wsp_file <- system.file("extdata", "gating.wsp", package = "FlowSOM")

# Specify the cell types of interest for assigning one label per cell
cell_types <- c("B cells",
                "gd T cells", "CD4 T cells", "CD8 T cells",
                "NK cells","NK T cells")

# Parse the FlowJo workspace   
library(flowWorkspace)             
gatingResult <- GetFlowJoLabels(fcs_file, wsp_file,
                                cell_types = cell_types)

# Check the number of cells assigned to each gate
colSums(gatingResult$matrix)

# Build a FlowSOM tree
flowSOM.res <- FlowSOM(fcs_file, 
                       compensate = TRUE, 
                       transform = TRUE,
                       toTransform = 8:18, 
                       colsToUse = c(9,12,14:18),
                       nClus = 10,
                       seed = 1)
   
 # Plot pies indicating the percentage of cell types present in the nodes
 PlotPies(flowSOM.res$FlowSOM,
          gatingResult$manual,
          backgroundValues = flowSOM.res$metaclustering)

FlowSOM documentation built on Nov. 8, 2020, 6:40 p.m.